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Owen Queen

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4 papers

2 author rows

NeurIPS Conference 2025 Conference Paper

CGBench: Benchmarking Language Model Scientific Reasoning for Clinical Genetics Research

Owen Queen
Harrison Zhang
James Zou

Variant and gene interpretation are fundamental to personalized medicine and translational biomedicine. However, traditional approaches are manual and labor-intensive. Generative language models (LMs) can facilitate this process, accelerating the translation of fundamental research into clinically-actionable insights. While existing benchmarks have attempted to quantify the capabilities of LMs for interpreting scientific data, these studies focus on narrow tasks that do not translate to real-world research. To meet these challenges, we introduce CGBench, a robust benchmark that tests reasoning capabilities of LMs on scientific publications. CGBench is built from ClinGen, a resource of expert-curated literature interpretations in clinical genetics. CGBench measures the ability to 1) extract relevant experimental results following precise protocols and guidelines, 2) judge the strength of evidence, and 3) categorize and describe the relevant outcome of experiments. We test 8 different LMs and find that while models show promise, substantial gaps exist in literature interpretation, especially on fine-grained instructions. Reasoning models excel in fine-grained tasks but non-reasoning models are better at high-level interpretations. Finally, we measure LM explanations against human explanations with an LM judge approach, revealing that models often hallucinate or misinterpret results even when correctly classifying evidence. CGBench reveals strengths and weaknesses of LMs for precise interpretation of scientific publications, opening avenues for future research in AI for clinical genetics and science more broadly.

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NeurIPS Conference 2024 Conference Paper

UniTS: A Unified Multi-Task Time Series Model

Shanghua Gao
Teddy Koker
Owen Queen
Thomas Hartvigsen
Theodoros Tsiligkaridis
Marinka Zitnik

Although pre-trained transformers and reprogrammed text-based LLMs have shown strong performance on time series tasks, the best-performing architectures vary widely across tasks, with most models narrowly focused on specific areas, such as time series forecasting. Unifying predictive and generative time series tasks within a single model remains challenging. We introduce UniTS, a unified multi-task time series model that utilizes task tokenization to integrate predictive and generative tasks into a single framework. UniTS employs a modified transformer block to capture universal time series representations, enabling transferability from a heterogeneous, multi-domain pre-training dataset—characterized by diverse dynamic patterns, sampling rates, and temporal scales—to a wide range of downstream datasets with varied task specifications and data domains. Tested on 38 datasets across human activity sensors, healthcare, engineering, and finance, UniTS achieves superior performance compared to 12 forecasting models, 20 classification models, 18 anomaly detection models, and 16 imputation models, including adapted text-based LLMs. UniTS also demonstrates strong few-shot and prompt capabilities when applied to new domains and tasks. In single-task settings, UniTS outperforms competitive task-specialized time series models. Code and datasets are available at https: //github. com/mims-harvard/UniTS.

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ICML Conference 2023 Conference Paper

Domain Adaptation for Time Series Under Feature and Label Shifts

Huan He
Owen Queen
Teddy Koker
Consuelo Cuevas
Theodoros Tsiligkaridis
Marinka Zitnik

Unsupervised domain adaptation (UDA) enables the transfer of models trained on source domains to unlabeled target domains. However, transferring complex time series models presents challenges due to the dynamic temporal structure variations across domains. This leads to feature shifts in the time and frequency representations. Additionally, the label distributions of tasks in the source and target domains can differ significantly, posing difficulties in addressing label shifts and recognizing labels unique to the target domain. Effectively transferring complex time series models remains a formidable problem. We present RAINCOAT, the first model for both closed-set and universal domain adaptation on complex time series. RAINCOAT addresses feature and label shifts by considering both temporal and frequency features, aligning them across domains, and correcting for misalignments to facilitate the detection of private labels. Additionally, RAINCOAT improves transferability by identifying label shifts in target domains. Our experiments with 5 datasets and 13 state-of-the-art UDA methods demonstrate that RAINCOAT can improve transfer learning performance by up to 16. 33% and can handle both closed-set and universal domain adaptation.

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NeurIPS Conference 2023 Conference Paper

Encoding Time-Series Explanations through Self-Supervised Model Behavior Consistency

Owen Queen
Tom Hartvigsen
Teddy Koker
Huan He
Theodoros Tsiligkaridis
Marinka Zitnik

Interpreting time series models is uniquely challenging because it requires identifying both the location of time series signals that drive model predictions and their matching to an interpretable temporal pattern. While explainers from other modalities can be applied to time series, their inductive biases do not transfer well to the inherently challenging interpretation of time series. We present TimeX, a time series consistency model for training explainers. TimeX trains an interpretable surrogate to mimic the behavior of a pretrained time series model. It addresses the issue of model faithfulness by introducing model behavior consistency, a novel formulation that preserves relations in the latent space induced by the pretrained model with relations in the latent space induced by TimeX. TimeX provides discrete attribution maps and, unlike existing interpretability methods, it learns a latent space of explanations that can be used in various ways, such as to provide landmarks to visually aggregate similar explanations and easily recognize temporal patterns. We evaluate TimeX on eight synthetic and real-world datasets and compare its performance against state-of-the-art interpretability methods. We also conduct case studies using physiological time series. Quantitative evaluations demonstrate that TimeX achieves the highest or second-highest performance in every metric compared to baselines across all datasets. Through case studies, we show that the novel components of TimeX show potential for training faithful, interpretable models that capture the behavior of pretrained time series models.

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